Well, I don't know about Zelda because we've seen very little of it, but after spending 65 hours playing Xenoblade X, all I can say is: Man, I wish it was really empty sometimes! xD
I hope this is not an SPOILER but, have you played in Sylvalum and Cauldros? I'm scared everytime I need to go to sylvalum because it's really full of enemies everywhere and everything just want to fucking kill you! I spend half the time there running away from enemies who see me and start going after me, and then another one joins in, and another... it gets on my nerves, I'm level 46 and I die so fast there it's shameful xD
I'm ok with Zelda U being this empty, honestly. The game will have lots of things to do, that's for sure, but if it's so big, I wouldn't mind if it wasn't everything packed with enemies.
I still think that in Zelda U the problem will be at night, when all the freaks and beasts will come out to eat you :P
If you want to explore and enjoy the views while having little to none threats: daytime is your thing.
If you're looking for trouble and you feel like suicidal then it's night time for you.
Everyone wins.
